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\newcommand{\theme}{ Observation, Modeling, and Control for Life Sciences}
\newcommand{\project}{MODEMIC}
\newcommand{\evaldate}{October 2013}
\newcommand{\prevevaldate}{October 2009}

\title{\sf INRIA, Evaluation of Theme \\ \theme }
\author{Project-team \project }
\date{\evaldate }

\begin{document}
\maketitle
\subsection*{Project-team title:}  Modelling and Optimisation of the Dynamics of Ecosystems with MICro-organisms
\subsection*{Scientific leader:} Alain Rapaport
\subsection*{Research center:}  INRIA-Sophia-Antipolis Méditerranée
  (Montpellier antenna)
\subsection*{Common project-team with:} INRA-MIA (Applied Mathematics and
  Informatics Department), UMR MISTEA Montpellier

\section{Personnel}
\subsection*{Personnel (\prevevaldate )}


\begin{center}
\begin{tabular}{|c|c|c|c|c|c|} \hline
                             & Other EPST  & INRIA & INRA & University & {\bf Total} \\ \hline \hline
DR (1) / Professors          &        &       &  1   & 1	& {\bf 2} \\ \hline
CR (2) / Assistant Professors& 	      & 3     & 1	& 
& {\bf 4} \\ \hline
Permanent Engineers (3)      & 	 & 	 & 	& 	& {\bf} \\ \hline
Temporary Engineers (4)      & 	 & 	 & 	& 	& {\bf} \\ \hline
PhD Students                 & 3.5	 & 0.5	 & 1	& 1	& {\bf
6} \\ \hline
Post-Doc.                    & 2	 & 	 & 	& 	& {\bf
2} \\ \hline
{\bf Total}                  &{\bf 5.5}   &{\bf 3.5}  &{\bf 3}	& {\bf
1} & {\bf 13} \\ \hline
External Collaborators       & 	 & 	 & 	& 	& {\bf
} \\ \hline
Visitors ($>1$ month)        & 	 2 & 	 & 	& 1	& {\bf 3 } \\ \hline
\end{tabular}
\end{center}

(1) ``Senior Research Scientist (Directeur de Recherche)''

(2) ``Junior Research Scientist (Charg\'e de Recherche)''

(3) ``Civil servant (CNRS, INRIA, ...)''

(4) ``Associated with a contract (Ing\'enieur Expert or Ing\'enieur Associ\'e)'' 

\subsection*{Personnel (\evaldate )}

\begin{center}
\begin{tabular}{|c|c|c|c|c|c|} \hline
 			     & Other EPST & INRIA & INRA & University & {\bf Total} \\ \hline \hline
DR / Professors 	     & 	     & 1	& 2	& 1
& {\bf 4} \\ \hline
CR / Assistant Professor     & 	     & 	       & 1	& 0.5+0.5	& {\bf
2} \\ \hline
Inria Starting Position    & 	& 	& 	& 	& {\bf} \\ \hline
Permanent Engineer 	     &	& 	& 	& 	& {\bf} \\ \hline
Temporary Engineer 	     & 	& 	& 	& 	& {\bf} \\ \hline
PhD Students   		     & 7.5	& 	& 0.5+0.5	&0.5	& {\bf
9} \\ \hline
Post-Doc.	 	     & 	& 1	& 	& 	& {\bf 1} \\ \hline
{\bf Total}  		     & {\bf 7.5}&{\bf 2}  &{\bf 4}  &{\bf 3}  &
{\bf 16} \\ \hline
External Collaborators       & 3	& 1	& 	&	& {\bf
4} \\ \hline
Visitors ($>1$ month)        & 	& 	& 	& 	& {\bf} \\ \hline
\end{tabular}
\end{center}



\subsection*{Changes in staff}

%{\footnotesize\sl Number of scientific staff that joined or left the
%project-team during the last four years period or since the project creation.
%TBR.}

\begin{center}
\begin{tabular}{|c|c|c|c|c|c|} \hline
DR / Professors 		& Misc. & INRIA & INRA 	& University &
total \\ \hline
Arrival 			& 	& 1	& 1	& 		& 2\\ \hline
Leaving   			& 	& 	& 	& 		& \\ \hline\hline
CR / Assistant Professors 	& 	& 	& 	&
& \\\hline
Arrival 			& 	& 	& 1	& 0.5+0.5
& 2 \\ \hline
Leaving   			& 	& 3	& 1	&
& 4 \\ \hline\hline
Inria Starting Positions 	& 	& 	& 	&
& \\   \hline
Arrival 			& 	& 	& 	& 		& \\ \hline
Leaving   			& 	& 	& 	& 		& \\ \hline
\end{tabular}
\end{center}


\subsection*{Current composition of the project-team (October 2013):}
\noindent Permanent members:
\begin{itemize}
\item[] Fabien Campillo, DR INRIA
\item[] Céline Casenave, CR INRA 
\item[] Jér\^ome Harmand, DR INRA
\item[] Claude Lobry, Prof. emeritus, Univ. Nice
\item[] Alain Rapaport, DR INRA (team leader)
\end{itemize}
Part time members:
\begin{itemize}
\item[] Terence Bayen, Assistant Prof., Univ. Montpellier II
\item[] Marc Joannides, Assistant Prof., Univ. Montpellier II
\end{itemize}
External collaborators:
\begin{itemize}
\item[] Guillaume Deffuant, DR IRSTEA (LISC, Clermont)
\item[] Annick Lesne, DR CNRS (Paris VI)
\item[] Antoine Rousseau, CR INRIA (EPI MOISE, Grenoble)
\item[] Tewfik Sari, Prof. Univ. Haute Alsace (detached at IRSTEA
  Montpellier since 2011)
\end{itemize}
PhD students:
\begin{itemize}
\item[] Amine Charfi (Coadvise grant): Coadvisor: J. Harmand.
\item[] Coralie Fritsch (MESR and INRA grant): Advisor: F. Campillo.
\item[] Amel Ghouali (AVERROES grant): Advisors: J. Harmand and T. Sari.
\item[] Angelo Raherinirina (LIRIMA grant): Advisor: F. Campillo.
\item[] Radhouane Fekih-Salem (AVERROES grant): Advisors: A. Rapaport
  and T. Sari.
\item[] Guilherme Pimentel (U. Mons and INRA grant): Coadvisor: A. Rapaport.
\end{itemize}
PhD students in other teams co-advised by some member of MODEMIC :
\begin{itemize}
\item[] Walid Bouhafs (LAMSIN, Tunisia). Coadvisor: J. Harmand.
\item[] Lamine Mamadou Diagne (U. de Mulhouse AUF grant). Coadvisor: T. Sari.
\item[] Sonia Hassam (Univ Tlemcen and POLIMI). Coadvisor: J. Harmand.
\end{itemize}
Post-doc:
\begin{itemize}
\item[] Matthieu Sebbah (CIRIC-INRIA Chile grant)
\end{itemize}

\subsection*{Current position of former project-team members (including PhD students during the (2010-2013)  period):}

%{\footnotesize\sl Provide a list of former project-team members including name,% current position, name and location of the employer. TBR.}

\begin{description}
\item Nabil Mabrouk, after defended his PhD in January 2010, has been
  recruited as an engineer at LISC (IRSTEA Clermont) in the ANR
  project DISCO, conducted by the team. He is presently project
  manager at Propespol.
\item Miled El Hajji has defended his PhD in December 2010 at
  U. Montpellier, and is now Research Assistant at U. Sousse
  (Tunisia).
\item José Fernandez, after begun to prepare his PhD in the team, in
  cotutelle with Chile since 2009, has had to stop due to health
  problems, and has returned to Chile.
\item Ihab Haidar has defended his PhD in December 2011 at
  U. Montpellier. He is currently postdoc at SupElec, Gif-sur-Yvette.
 \item Nabil Mabrouk PhD sustained in january 2010 co-avised by MERE and LISC (G. Deffuant).
\item Alhem Saddoud, after her postdoc in the team 2010, has returned to
  U. Sfax (Tunisia), where
  she has a position of Research Assistant.
\item Boum\'edienne Benyahia has defended his PhD in December 2012 at
  U. Tlemcen and is
  now Research Assistant at Univ. Tlemcen (Algeria).
\item Bart Haegeman (CR INRIA) is detached at CNRS (Station
d'\'ecologie exp\'erimentale de Moulis) since September 2012.
\item After her postdoc in the team in 2011 and 2012, Chlo\'e Deygout has
  been recruited at ANR in January 2013.
\end{description}

\subsection*{Last INRIA enlistments}

%{\footnotesize\sl Provide a list of INRIA researchers who have been hired in th%e project-team including name, year of recruitment and position (CR2, CR1, DR2,% DR1). TBR.}

\begin{description}

\item Tewfik Sari (Prof. Univ. Haute Alsace) has been in INRIA delegation
  during two years and an half (until July 2011).
\item Térence Bayen (Assistant Prof. Univ. Montpellier II) has been in INRIA delegation
  during one year (until August 2013).

\end{description}


\subsection*{Other comments:}

%{\footnotesize\sl State in this section any modification relevant to
%the projec%t-team such as a change of the scientific leader or any
%other information you w%ould like to add.  For instance, you may also
%want to list the PhD students who% have arrived after the last
%evaluation and have left after this evaluation, if% any,  since they
%are not counted in the personnel tables above, even though th%eir
%names can be found in your activity periods over the evaluation
%period. TBR%.}

MODEMIC is the continuation of the former team MERE, that has
been funded and managed by Prof. Claude Lobry.
Due to the retirement of C. Lobry, MERE has been stopped at the end of
the year 2010. MODEMIC has been proposed in 2011 and officially created
in January 2012.\\

Some changes in  the positions of the members of the team
have occurred during the evaluation period:
\begin{description}
\item Fabien Campillo (INRIA) has been promoted Directeur de recherche in
  2010.
\item Jér\^{o}me Harmand (INRA) has been promoted Directeur de recherche  in
  2011.
  \item Bart Haegeman was a permanent member of former MERE and now of MODEMIC. Since September 2012 he is detached  in a CNRS laboratory of ecology.
   \item C\'eline Casenave was recruited in September 2011. She has a Ph.D. in Automatic Control and she worked as a post-doctoral fellow at the CESAME, in Belgium, during one year before her recruitment. Her post-doctorate supervisor, Denis Dochain, is a long term collaborator of the MERE/MODEMIC project-team. 

\end{description}
 
\section{Work progress}

\subsection{Keywords} 

\noindent {\em Methodological keywords:} mathematical and computer modelling,
dynamical systems, differential equations, PDEs, stochastic processes,
integro-differential equations, population models, model
reduction, automatic control, filtering and identification.\\

\noindent {\em Applications keywords:} microbiology, microbial ecology,
bio-technology, waste-water treatment.

\subsection{Context and overall goal of the project}
%{\footnotesize\sl develop a structured view of the research program
%rather than simply presenting a set of ideas to be explored. TBR.}\\

In the complex processes of material and energy transformations on
earth, the microbial compartment is crucial for major biochemical
cycles, that sustain life on Earth and regulate the climate.
There are presently growing
social demands for the preservation of water quality, the 
regeneration or soil fertility or the development of new ecosystem
services for the environment, for which micro-organisms are necessary.
Therefore, knowledge, control and management of microbial ecosystems
appear to be essential to satisfy such expectations. Aside
observations and experiments, modeling and computer simulations
have an important role to play in the fields of microbiology and
microbial ecology.\\ 


In this context, MODEMIC aims at sharing skills of INRA and INRIA
researchers for developing, analyzing and simulating new models of microbial
ecosystems as efficient tools to understand, explore, pilot and manage
natural or industrial bio-processes.

For this purpose, we study mathematical and/or computer models
of the dynamics of populations of micro-organisms. These models can be
complex or reduced ones. We carry simulations and possibly
mathematical analyses. We put an emphasis on the understanding
of the dynamical properties out of equilibrium, because most of 
real processes represented by these models are either out of
equilibrium, or one needs to predict which equilibrium is
reached.

For applications with industrial perspectives, we propose control
strategies and identification techniques of these models, with
the tools of Automatic Control for state space systems.\\


The MODEMIC team has proposed its ``four years objectives'' when he was
formally created only two years ago. But MERE was stopped four years
ago and since this date, during the transition,  the team was animated
by A. Rapaport. As a consequence we present a whole synthesis of our
activities since 2010 following the five objectives formulated in
2012. It should be underlined that B. Haegeman is responsible for an
important scientific success of MERE obtained in collaboration with
J.-J. Godon and his team from the LBE (INRA lab at Narbonne). This
work, initiated by J. Harmand was widely depicted in the activity
synthesis report of 2009. Due to delay in publication and
administration, one publication and one patent \cite{Art160,Misc19}
related to that work are still visible in the present report. On the other hand, since 2010 his scientific work was definitely oriented toward theoretical ecology and, by the way, have become completely separated from MODEMIC's objectives. His corresponding publications \cite{Art42,Art43,Art45,Art70,Art71,Art72,Art74,Art76,Art142} are quoted in our list of publications but we will not explain their scientific content and, obviously, not count them in our balance.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Objective 1: build, simulate and analyse new models of microbial
ecosystems}\label{objectif 1}

\noindent {\em Permanent researchers:}
Fabien Campillo, Céline Casenave, Jér\^{o}me
Harmand,  Claude Lobry, Alain Rapaport , Tewfik Sari.\\

\noindent {\em PhD students:} Boumédiène Benyahia, Miled El Hajji, Radhouane Fekih
Salem, Coralie Fritsch, Ihab Haidar, Guilherme
Pimentel, Angelo Raheriniria.\\

\noindent {\em Postdoc fellows:} Chlo\'e Deygout, Alhem Saddoud.

\subsubsection{Project-team positioning}

We study population models of micro-organisms and their computer simulations,
with the objective of better understanding and prediction of the
dynamics of microbial ecosystems, with a particular emphasis on situations outside equilibrium. 
The main questions we address concern the roles of biotic and abiotic
interactions on the coexistence or exclusion of species, the behavior of
transient dynamics and the performances of bio-processes. 

Our positioning is half-way between biomathematics and computer sciences, on one side, and 
bio-processes modeling, on the other one, that we believe to be original compared to
teams such as, for instance, CESAME (U. Louvain-la-Neuve) or BIOEMCO (Paris Grignon). Our approach and background have similarities
with the BIOCORE INRIA project-team, but we carry specific interests on biodiversity and spatial considerations.\\
\subsubsection{Scientific achievements}
The chemostat model is quite popular in microbial ecology and
bio-process engineering, and often serves as a starting point for
modelling tasks. Therefore, the team carries a significant activity about
generalisations and extensions of this model. 
\begin{description}
\item New results about species coexistence under general hypotheses have
been obtained.
In   \cite{Art134,Art164,Art136} 
The theorem known as ``Competitive Exclusion Principle'' has been generalised to a
large class of functional response and variable yields. This is a
significant  mathematical contribution toward the solution of an old conjecture concerning the competitive exclusion principle\footnote{
H.L. Smith, P. Waltman,
``The Theory of the Chemostat, Dynamics of Microbial Competition''.
Cambridge University Press, 1995.}.
At the opposite, in the PhD work of R. Fekih-Salem, conditions on intra and
inter-specific interactions terms have been given to provide species
coexistence \cite{Art50}.
\item In the framework of  the PhD of I. Haidar, properties of the input/output maps of
interconnected chemostats have been investigated,
motivated by simple representations of spatial heterogeneity
\cite{Art77,Art78,Draft9}, having
soil ecosystems in mind. The existence of thresholds on the input
concentration of the resource for which either serial either parallel
interconnections are the most efficient has been shown. This study encompasses the
dead-zone models of the literature.
\item Among the work of the PhD of R. Fekih-Salem, compartments of
free and aggregated biomass are distinguished in the classical chemostat model, as representations
of planktonic bacteria and flocks or  biofilms.
Non-intuitive dynamical behaviors have been characterized under the hypotheses that attachment and
detachment dynamics are fast compared to biological ones. It has been shown that such dynamics can exhibits bi-stability
even though growth functions are monotonic, which is new compared to
the chemostat model with undifferentiated biomass \cite{Art48}.
\item  In the framework of  the PhDs of B. Benyahia and R. Fekih-Salem, mathematical
analyses of models of anaerobic digestion processes have been
performed \cite{Art8,Art166}, and recently extensions including the 
fouling dynamics of membrane reactors have been investigated \cite{Art9}. 
\item The chemostat revisited \cite{Art18,Art19}.
 The chemostat dynamics are classically represented by a system of ordinary differential equations. Our goal in these papers is to establish a stochastic model that is valid at the scale immediately preceding the one corresponding to the deterministic model. 
 At a microscopic scale we present a pure jump stochastic model that gives rise, at the macroscopic scale, to the ordinary differential equation model. At an intermediate scale, an approximation diffusion allows us to propose a model in the form of a system of stochastic differential equations. We expound the mechanism to switch from one model to another, together with the associated simulation procedures. We also describe the domain of validity of the different models. This work is very closely related to our investigations in the domain of simulation algorithms 
 (see section \ref{objectif 4}).
 \item Miscellanies. Papers \cite{Art39,Art109,Art135,Art162,Draft3} are punctual
   contributions in ecological modeling related to various
   collaborations.


\end{description}


\subsubsection{Collaborations}
All these research are intimately connected with TREASURE network and  DISCO network (see section \ref{objectif 5})
\subsubsection{External support}

At the national level: ANR~: MODECOL, DIMIMOS and DISCO, RNSC: MNMs, LABEX: Numev.\\

At the international level: Euro-Mediterranean 3+3: TREASURE,
SticAmsud: MOMARE, LIRIMA: STIC-Mada and NuWat.\\

\subsubsection{Self assessment}
The contributions depicted in this objective are in the very tradition of MERE and must be viewed as contributions to biomathematics, more precisely population dynamics. 
Some of these contributions are of high quality and published in good
journals. Modeling of the consequences of floculation process in the
dynamic of the chemostat is promising since they put in light new
qualitative phenomena. The two publications associated to I. Haidar
thesis sho our progress in the new orientation of
MODEMIC in the direction of soils microbial ecology. More recently,
C. Casenave has also invested in this direction with UMR Eco\& Sols (Montpellier).
We consider this activity more or less as ``routine activity'', not to
risky but not open to great novel achievements. We need such an
activity since our Objective 4 is ambitious and, by the way, much more
risky.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%{\red On attend la contribution de J\'er\^ome qui devrait contenir l'essentiel du travail de C\'eline sauf, peut \^etre le travail sur le process "vin" qui pourrait avoir sa place dans objectif 3 \`a voir.}

\subsection{Objective 2:  validate hypotheses and identify models with experimental
data.}
\label{objectif 2}

%{\footnotesize\sl List of the permanent researchers and the PhD
%students involved in the work related to this objective (1-2
%lines). TBR.}\\

\noindent {\em Permanent researchers:}
Fabien Campillo, C\'eline Casenave, J\'er\^{o}me
Harmand, Alain Rapaport.\\

\noindent {\em PhD students:} Boum\'edi\`ene Benyahia, Amel Ghouali, Miled El Hajji,
Guilherme Pimentel.\\



\subsubsection{Project-team positioning}
%{\footnotesize\sl Should be about half a page. Positioning of the
%project wrt the state of the art and with regards to other INRIA
%project-teams and other national/international research groups (peer
%or competitor groups). TBR.}\\

The team has always had close relationships with microbiologists, agronomists
and process engineers, notably - but not only - from INRA. 
%Over the last years, this proximity has provided several
%opportunities to deal with experimental data at various scales.
%We focus on situations for which models can bring complementary
%knowledge or lightning over statistical treatments. 
%From a very general
%point of view, efforts were put on very specific questions
%arising from exchanges with microbiologists or process engineers.
For instance, we put much efforts on the study
and on the characterization of biotic interactions within complex
microbial ecosystems. 

Our main objective is never simply to match data with a dynamical system.
Rather, our collaborations with specialists lead either to the qualitative validation of
models (that often enrich the theoretical questioning of
Objective 1), or to the quantitative identification of models (that can then be used
for control design, which specific syntheses are developed within Objective 3).
The main characteristics of the data we worked with are the following.
\begin{description}
\item[-] We mostly process data acquired at a population level. It is thus very different of what  
bioinformatic does, this latter working usually more with data obtained at the level of individuals.
\item[-] We work with time-series data in such a way we do not use statistical analysis
as the most pertinent way of analyzing them but rather use modeling and
identification techniques to come up with dynamical stochastic or deterministic models
that can be analyzed within activities of Objectives 1 or 3.

\end{description}

\subsubsection{Scientific achievements} 

A routine, but important activity consists in the application of deterministic
observers (also called “software sensors”), stochastic filtering and
identification to various
problems. We aim also at considering multi-valued or probabilistic identification
when
usual approaches fail. Compared to activities of teams such as LAGEP (INSA Lyon),
L2S (Supélec Gif-sur-Yvette), or INRIA project team BIOCORE which have similar
approaches, we focus on multi-strains microbial ecosystems \cite{Art123} or ``complex'' bioprocesses \cite{Art165}.\\

The team has had various original contributions about the extraction of valuable
information
from experimental data and practical model identification. Within its
collaborations with
microbiologists, several kinds of observations are met at different scales,
leading to dedicated treatments of the data:
\begin{description}
\item[-] {\em Macroscopic sensors and observers.}
In industrial bio-processes, the inhibition growth by an excess of
substrate
is often an issue in model identification because of the presence of unstable
modes. In
\cite{Art137}, an adaptive control law coupled with a continuation technique has been
proposed for
the functional reconstruction of unknown growth curves, without any a priori
knowledge on
their monotonicity. 

In soil microbiology, batch experiments are often used
instead of continuous cultures. In such a case, nutrient recycling is often not negligible. In
this framework,
a cascade observer with a practical convergence, due to the lack of observability
at steady
state of the model, has been proposed \cite{Proc106}.
In \cite{Proc124}, coupling information provided by molecular
fingerprints and optimal biomass density together with observers, we have
proposed a procedure to identify the functions of major species within complex ecosystems of
nitrifying
chemostats. 


\item {\em Confrontation of models to virtual data.}
The qualitative studies of models described in Objective 1 highlight the
importance
of the nature and shape of the species interactions in process performances. The
practical
estimation of these interactions in microbial ecosystems remains today an issue
and a
challenge. From particular experiments driven in soil ecosystems, that consist in
measuring
performances of random samples of different diversity, it has recently been shown
that
some characteristics on the nature and the number of species interactions in the
original
ecosystem could be inferred from the shape of the curve diversity/performance
and assembling models (publication
under revision).
As experiments are often costly and time consuming, we conduct also comparisons
of
our “simple” models (for instance with over-simplified spatial representations,
see Objective 1) with the output of “realistic” simulation software, such as MIN3P (for
biochemical
transfers in soils) \cite{Art77} or solvers of Navier-Stokes equations
(for inhomogeneous water resources) \cite{Misc28}.

\item {Molecular fingerprints and genomic data.}
Molecular techniques generate a very high quantity of data. For genomic data, it has been shown in \cite{Art88} that the size of pan
and core
genomes in microbial populations can be estimated given a small number of
sequenced
genomes. Finally, from a purely taxonomic view point, it has been shown in \cite{Art160}
that estimating the diversity is intrinsically problematic for highly diverse
communities, because
of the presence of rare species: the Hill diversity $D_{\alpha}$ can be robustly estimated
provided
that its index $\alpha$ is above one. The former contributions of the team about the
estimation
of the diversity of an microbial ecosystem from signals provided by molecular
fingerprints
have led to a patent deposit \cite{Misc19}.

\item {\em Statistical signal processing.}
We have proposed a statistical procedure that takes into account experimental replica
in case of extinction for bacterial growth studies \cite{Draft18}.

\end{description}

\subsubsection{Collaborations}

On these questions our main collaborations are through DISCO (see section \ref{objectif 5}) and some through TREASURE and DYMECOS.

Regarding soil ecosystems, we work with several INRA labs: UMR Eco\&Sols (Montpellier),
INRA UREP (Theix), MSE (INRA Dijon) and UMR BIOEMCO (co-supervisions
of the PhD of M. El Hajji and I. Haidar, publications \cite{Proc106,Art123,Inbook4,Art77,Art78}.
These collaborations have been initiated within the ARC VITELBIO.\\


On the methodological aspects, we mainly exchange with U. Louvain-la-Neuve
(D. Dochain), U. Exeter (J. Sieber), EPI SISYPHE
(M. Desroches, U. Mons (A. Vande Wouver) and EPI MOISE
(A. Rousseau).

\subsubsection{External support}

ANR DIMIMOS and DISCO, ARC VITELBIO, RNSC E-MICRAM, CNRS PEPI ASYDE and
INRA meta-program ENOC are our main projects for what concerns this Objective 2.

\subsubsection{Self assessment}

We had some difficulties to provide a synthetic report for this objective.
This is undoubtedly do to the fact that the first point of its title:
{\em validate hypotheses and identify models with experimental
data},
that is to say ``validate hypothesis'', is an objective for theoretical biologists or ecologists, which
{\em we are not}. By the way it is difficult for us to appreciate to what extend such an objective is achieved.
Moreover, the second term ``identification'' is not an objective in itself but rather a routine activity which 
depends much on opportunities.

The team has initiated the opportunities of developing multi-scale approaches, notably through 
the coordination of the DISCO project. We
believe that this is a very strong point, and presently an original feature
in the context of microbiology and hope concrete achievements in the near future.

Many important contributions on data processing and on the interpretation of
signals from molecular fingerprints have been obtained by the team MERE (and
especially a patent). As those techniques evolve very quickly, this
dimension is less present in MODEMIC team and the subject is more or less on its end.

Of course, from a very general point of view, we greatly 
depend on our microbiologists colleagues for data acquisition.
Several experimental setups that are
suggested by the analyses of the models, in view of the validation of
their hypotheses, are often not available
for technical or manpower reasons (continuous cultures are much more
difficult to be conducted than batch cultures). This is particularly
the case in the domain of soil ecosystems where continuous
culture are usually not used (UMR MSE Dijon, UMR Eco \& sols,
Montpellier).
Situation has been easier within the
DISCO project: experiments at IRSTEA HBAN (Antony) on flowcell experiments 
were conducted on the basis of simulation results.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{Objective 3: propose new strategies to pilot and
  optimise microbial ecosystems.}
\label{objectif 3}

\subsubsection{Personnel}


\noindent {\em Permanent researchers:}
Terence Bayen, Céline Casenave, Jér\^{o}me Harmand, Alain Rapaport.\\

\noindent {\em PhD students:} Boumédiène Benyahia, Amel Ghouali, Miled
El Hajji, Guilherme Pimentel.\\

\noindent {\em Postdoc fellow:} Matthieu Sebbah.


\subsubsection{Project-team positioning}

Among most of our collaborations about industrial bio-processes (waste-water treatments, food fermentation...), we often met questions related to the piloting, design or supervision of bio-processes that we aim at consider at both methodological and applied levels. For this purpose, we consider classical or original models developed along Objectives 1 and 2 to propose new control or design strategies.\\

Practically, we search for state or output feedback strategies for stabilizing bio-processes, or optimizing paths with respect to criteria such as minimum time. We focus on the derivation of global
controllers based on the nature of non-linearity and input
constraints (such as positivity of the manipulated variables), and investigate how these realizations can be applied under uncertainties on
both model and measurements (using for instance extremum-seeking techniques). Our main goal is to provide satisfactory 
solutions (optimal or sub-optimal) relevant to be implemented on real processes that possesses a limited number of sensors. Compared to activities of INRIA project teams such as COMMANDS or McTao, our work is more dedicated to the specific dynamics of bioreactors.\\

The design of bio-processes by decoupling the residence time of micro-organisms in several interconnected tanks is very promising in terms of performances, which is already known in industrial frameworks, but often with empirical rules.
We aim at investigating more deeply these questions, that are strongly related to the topics of sparse representations of spatial inhomogeneity described in Objective 1.  

Aside this theoretical activity we aim at modeling, identify and control process laboratories. This is said in few words but needs a lot of time !

\subsubsection{Scientific achievements}

Aside stabilization results based on controlled Lyapunov functions,
we have more intensively, mainly since T. Bayen delegation, invested
on the study of minimal time control problems 
\cite{Art159,Art51,Art115,Art125,Art163,Draft12,Draft13,Draft2}. 
Although the theory of optimal control is not an objective by itself for the team, it turns out that the study of minimal time is a way to get information on the controllability of systems, and to obtain stationary state feedbacks.
Most of the time, our control problems are linear with respect to the
control variable, which implies that singular arcs play an important
role, and we focus on characterizing their global optimality.
Other questions related to system theory, notably software sensors
(observers) are addressed in \cite{Draft10} for extremum seeking
problems under uncertainties.
At the same time, we also worked on some real experimental processes.\\\\
Within the framework of the European CAFE project, we also have studied the problem of control of a cascade of bioreactors. An experimental setup of four tanks connected in series has been designed by the research unit SPO (Sciences Pour l'Oenologie,  Montpellier) to mimic batch wine making fermentation, and study the yeast at stable physiological stages. The modeling, identification and control of this actual process is done by C. Casenave.The goal of the problem under consideration is to control the sugar concentration in each tank of the process. The control inputs are the input flow rates $Q_{i}$ of each reactor. The originality of the problem lies in the cascade structure of the process, which leads to some constraints on the inputs $Q_{max}\geq Q_{i}\geq Q_{i-1}\geq 0$. We have proposed a control strategy based on a linearizing feedback law coupled with a state observer to estimate the unmeasured sugar concentration. This control law has been validated on the experimental process \cite{Report4,Report5}. \\
The non usual constraint on the inputs leads to interesting new
theoretical questions on controllability which where studied by Jos\'e
Fernandez (before his illness) and are now studied by  M. Sebbah \cite{Draft2} in Chile.\\

An alternative for the stabilization of unstable bioprocesses by means
of manipulated variable such as the input flow (that imposes to have
an upstream storage during the transients) is to look for equivalent
processes with an interconnected structure that is ``passively''
stable i.e. without the need of any actuator. This is what we have
discovered from the simulations conducted in the VITELBIO project
 and that has led to a patent design \cite{Draft9,Misc27}.\\

Publications \cite{Art86,Art85,Art105} come from old collaborations and deal with viability analysis for the management of
natural resources, that are not related to microbial ecosytems.


\subsubsection{Collaborations}

We have an old collaboration with Univ. of Louvain-la-Neuve
(D. Dochain, who has been a long-term visitor of the team in the
past). In addition to some recent works \cite{Art125}, the team
is involved in the European project CAFE (see Section
\ref{section-international}) that is piloted by D. Dochain. Two kinds
of collaborations have been conducted for the control of real processes:
\begin{description} 
\item[-] with UMR SPO (Montpellier) and U. Louvain-la-Neuve (D. Dochain)
  for wine fermentation processes \cite{Report4,Report5}.
\item[-] with IRSTEA Antony (D. Leducq) and U. Louvain-la-Neuve
  (D. Dochain) for ice cream crystallization
  Just before she was recruited, C. Casenave already worked on a problem of control of an ice cream crystallization process. Even though there isn't any micro-organisms in the system, the model used to describe the crystallization phenomena is very close to the ones of microbial ecosystems. Indeed, to describe the evolution of the ice crystals, a population balance equation is considered, with nucleation, growth, breakage and transport terms. The problem under consideration was the control of the viscosity of the ice cream at the outlet of a continuous crystallizer. The main difficulties come from the few available measurements, and the measurement delay. We have proposed a nonlinear control strategy with the temperature of the refrigerant fluid of the crystallizer as control input. This control strategy is based on a linearizing control law coupled with a Smith predictor to compensate the measurement delay. The control has been validated on an experimental pilot plant located at IRSTEA (Antony, France) \cite{Proc28,Proc29,Report4,Report5}.\\
\end{description}

Several optimal control problems for fed-batch processes and preservation of natural resources have been studied within the INRIA Associated Team with Chile (see the project DYMECOS section \ref{objectif 5}).\\
 
For control and observation of bioprocesses, we have also common works with LAGEP (H. Hammouri), and more recently with U. Mons (A. Vande Wouver) about the control of membrane bioreactors (within the co-supervision of the PhD of G. Pimentel). A recent collaboration with U. Exeter (J. Sieber) and EPI SISYPHE
(M. Desroches) has begun about extremum seeking controllers.


\subsubsection{External support}
European project CAFE, Associated team with Chile DYMECOS, Euro-Mediterranean network TREASURE  and CNRS PEPI ASYDE.


\subsubsection{Self assessment}

Our participation to the European project CAFE has been very stimulating, and encourage us to participate to other such projects. Our visibility outside the academic world is still poor for considering projects or contracts directly with industries. Nevertheless, we hope that our two recent patent deposits could help us to have a better approach with industries (such as Veolia, Suez, Sanofi...).
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{Objective 4: develop a strategy of software production.}\label{objectif 4}


\subsubsection{Personnel}

\noindent {\em Permanent researchers:}  Fabien Campillo, Marc Joannides, Claude Lobry, Alain Rapaport, Tewfik Sari.


\noindent {\em PhD students:} Coralie Fritsch.

\noindent {\em Postdoc fellows:} Chlo\'e  Deygout.

\subsubsection{Project-team positioning}
Modeling and simulation of the dynamic of microbial ecosystems raise specific and original codes problems:
\begin{description}
\item[-] simultaneous presence in the same code of both continuous variables (concentration of chemicals or very large populations) and discrete (when the population has a very small number of individuals),
\item [-] simultaneous presence in the same code of stochastic aspects (for birth and death processes for instance) and deterministic ones (for macroscopic laws)
\item[-] use of I.B.M. models which are too time expensive when the number of individuals is large ( might be more than $10^{12}$ ).
\end{description}
We believe that these questions must be addressed in a rigorous mathematical framework\footnote{
We use the framework defined by : convergence of Markov processes with values in integer or real spaces (for population dynamics in size, biomass etc.) or with values in measures (for individual-based models) -- see e.g. the book of Ethier and Kurtz -- gives a very powerful setting for the analyses of stochastic population models and their links with deterministic counterparts). See the work of S. M\'el\'eard (and students), T. Kurtz, A; Etheridge etc.}
and that their solution is a formidable scientific challenge that will certainly not be achieved by our small team. It will occupy tens of teams during decades ! But we think that we belong to the pioneers.
\subsubsection{Scientific achievements}
\begin{description}
\item In the following papers: \cite{Art101}, \cite{Draft20},\cite{Art16,Draft15} one starts from I.B.M. models and try to deduce ``macroscopic'' laws in the limit when the number of individuals and/or time tend to infinity. The first two papers are in an heuristic style (called ``physicist style'' by pure mathematicians) and the two last papers in the very rigorous mathematical style within the framework of stochastic processes. In all cases we produce simulations, sometimes surprising.
\item In \cite{Art20} we consider a birth and death type model (approximated by a diffusion) where a parameter $\omega$ represents the number of individuals such that the limit model when $\omega$ tends to infinity is the classical Rosenzweig MacArthur deterministic differential system for which persistence holds. We show that even for $\omega = 10^6$ to $10^8$ the birth and death process goes to extinction in short time with high probability.
\item In \cite{Inbook6}, motivated by the fact that in a chemostat thousands of different species can coexist we consider a system of a great number of differential equations and explain surprising oscillation observed in simulation. In particular this shows that for certain questions approximation through continuous traits are not valid.


\item IBM of clonal plant dynamics: see Section \ref{section-software}.


\item IBM's for bacterial growth in the context of the ANR DISCO project:
see Section \ref{section-software}.

 \item In the framework of the ARC VITELBIO, a web service has been
   developed, that is dedicated to biologists that are not familiar
   with the simulation of models of dynamical systems. This software
   is currently used as a teaching support in Master classes.
\end{description}
\subsubsection{Collaborations}

 \noindent The DISCO network was essential . See section \ref{objectif 5}\\\\
The MODECOL project ( MOD\'elisation ECOLogique de prairies virtuelles) [ANR-08-SYSC-012] of the ANR Syscomm program (SYSt\`emes COmplexes et Mod\'elisation Math\'ematique) aimed at developing models for the dynamic of prairial ecosystem. Fabien Campillo was co-principal investigator for INRIA for the INRIA project-teams MODEMIC, ALEA and TOSCA. The task of the INRIA teams was to develop a model and a computer prototype for the dynamic of the growth of clonal plants. see\\

\subsubsection{External support}
 ANR DISCO, ANR MODECOL, ARC VITELBIO.

\subsubsection{Self assessment}
During the evaluation process of the project MODEMIC on of the referees (Sergio Rinaldi) wrote, with some humor, regarding the present objective :
\begin{quote}
{\em  In contrast, I am not so much convinced that the research team can significantly penetrate the market of software production for the study of ecosystem as stated at page 7. Indeed, for penetrating that market, professional expertise in producing software with images in motion, with colours and music, is required, an expertise that (fortunately!) is not detectable in the publication of the research team.}
\end{quote}
 In fact it seems that during the presentation of our objective we confused the ``production of software'' with what we effectively do:
a contribution to the production of pertinent codes for simulation. On the other hand, our experience of DISCO showed to us the the actual ``demand'' of potential users is very difficult to estimate. For the moment it does not seem pertinent to insists in this direction.

At some other place in the evaluation of the project the referees noticed our relative incompetence in the field of the discrete dynamics (IBM). If we think of our capacity to  implement big models of IBM type using all the resources of parallelism and  farms of computers the criticism remains valid. 
But, in contrast,  in the field of the theorizing of these tools in the appropriate mathematical framework of the stochastic dynamical systems, we think of making an innovative work called to develop as shown by this recent 
\href{http://smai.emath.fr/cemracs/cemracs13/Projets/EPIDEMIO-GD.pdf}{note} of E. Pardoux to CEMRACS 2013 ( Seminar of the Centre d'Et\'e de Math\'ematiques et de Recherche Avanc\'ee en Calcul Scientifique) and our contribution to the special issue \cite{Art141} of the journal Ecological Modelling''.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{Objective 5: disseminate and collaborate at national and
  international levels.}\label{objectif 5}


\subsubsection{Personnel}

\noindent {\em Permanent researchers:} all.\\

\noindent {\em PhD students:} all.\\

\noindent {\em Postdoc fellows:} all.\\

{\em It might seem strange to present as an ``objective'' for the team: ``disseminate and collaborate at national and
  international levels'' ! Is not it one of obvious objectives of any scientific activity? In reality we wanted to point  the fact that our activity rests very strongly (not to say exclusively) on our collaborations. It is a necessity because we cannot cover all the scientific fields involved by our problems, it is a strength because it make us collaborate with leading scientists, it is a weakness because, in a collaboration we do not master all the parameters. 
  
So we report here on our three main collaborations TREASURE, DISCO and DYMECOS.}

\subsubsection{Project-team positioning}
\noindent \textbf{TREASURE}\\
\noindent {\em Permanent researchers:} Fabien Campillo, Jér\^{o}me Harmand, Claude Lobry, Tewfik Sari \\
\noindent {\em PhD students:} Boum\'edienne Benyahia, Amine Charfi, Amel Ghouali, Radhouane Fekih-Salem, Walid Bouhafs, Sonia Hassam.\\
\noindent {\em Postdoc fellows:} \\

 The ``occidental'' model of water management, designed in the last century without constraints of sustainability and dominated by the growing mobilisation of all available resources (supply approach) is not suitable for current issues of water demand in the Mediterranean countries focusing particularly on the influence of pathogens and micro-pollutants on the environment. Among the many options given on behalf of integrated and sustainable territorial water (demand management, etc..), an interesting solution requires a paradigm shift of water use patterns by providing a resource management including recycling. From a vision in which water is released into the environment after use and the best treatment, the time has come to study technological solutions for its reuse, particularly in agriculture. In other words, the problem is to move from a treatment with discharge into the natural environment to an improved treatment with water reuse. This solution has the advantage of reducing significantly the pressure exerted on the water of quality whose exploitation would be limited to the drinking water supply. To meet this challenge, processes coupling the membrane techniques to biological processes (notably the anaerobic digestion because its capability to produce valuable energy) conceived under both socio-economic and agronomic constraints appear appropriate. \\

The TREASURE network aims at integrating knowledge on the modeling,
the control and the optimization of biological systems for the
treatment and reuse of waste-waters in countries submitted to semi-arid
climates under both socio-economical and agronomic constraints within
the actual context of global changes.\\

Initiated in 2006 J\'er\^ome Harmand,  Claude Lobry and Tewfik Sari within the framework of the INRIA $3+3$ Euro-Mediterranean program, the project is coordinated by Jér\^ome Harmand since 2008. Since 2011, it officially includes $10$ institutional partners from $7$ Mediterranean countries. All or part of its members meet on a quite regular basis one or two times a year to review the results and plan future research activity.\\\\
\noindent \textbf{DISCO}

\noindent {\em Permanent researchers:} Fabien Campillo, Jér\^{o}me Harmand, Claude Lobry, Alain Rapaport (group leader), Tewfik Sari.\\
\noindent {\em PhD students:} Coralie Fritsch\, Radhouane Fekih-Salem.\
\noindent {\em Postdoc fellows:} Chlo\'e Deygout.\\

Outside of the laboratory the micro-organisms are not often in the ideal situation of ``perfect mixing'' which is the basic assumption of the chemostat model. In the field micro-organisms make their own habitat through the creation of biofilms which represents up to 99\% of the total biomass.
 Both for fundamental reasons and practical ones (it is biofilms which fill pipelines!) the mode of growth of these biofilms is the concern of sophisticated experimental studies using finer and finer  observation tools. For his concern  the modeling of these complex systems begins but it remains late with regard to the accumulation of the data from observation.
The idea of DISCO was to create a national network gathering ``model builders'' from  different origins (mathematics, physics, computing) with scientists from experimental world. Since 2007 A. Rapaport started search of partners, established a consortium of 5 teams which, after a first fruitless attempt, obtained a significant financing of the ANR SYSCOM. During this contract the network was led by MODEMIC (A. Rapaport)\\\\
\noindent \textbf{DYMECOS (associated team with Chile)}\\
\noindent {\em Permanent researchers:} Fabien Campillo, Jér\^{o}me Harmand, Claude Lobry, Tewfik Sari, Térence Bayen (since september 2012).\\
\noindent {\em PhD students:} Jos\'e Fernandez (April 2009-April 2012)\\
\noindent {\em Postdoc fellows:} Matthieu Sebbah (part time in Chile).\\

Since the beginning of MERE, A. Rapaport had scientific collaborations in the domain of optimal control with Centro Modelamiento Matematico of the University of Santiago de Chile, a  world famous laboratory in applied mathematics. These collaborations extended to two Universities of Valparaiso, including questions of bio-processes and environmental ecology. This motivated the support of INRIA which created the associated team DYMECOS (2009-2012 ).\\

\subsubsection{Scientific achievements}
\noindent \textbf{TREASURE\footnote{\url{https://project.inria.fr/treasure/}}}
All the activities of TREASURE are detailed on its website.\\

 The main TREASURE achievements can be classified into $3$ kinds of activities:\\

\noindent \emph{Education and schools} An important activity of TREASURE is the organization of one or two seminars per year dedicated to both young and senior researchers of the different research labs involved. One objective is to provide a common scientific background given that the research realized within the network is fundamentally multi-disciplinary. Schools including courses on bioprocess engineering or mathematical modeling are regularly organized within these seminars and conceived for the largest possible audience.\\
 
\noindent \emph{Co-supervision of students} Another important activity
is dedicated to co-advising of PhD students. A typical `TREASURE PhD student' is a student preparing his PhD under the co-advising of two partners of the network. This way, she/he may benefit of expertise from different fields which each partner is specialized on and can take advantage of exchanges under the form of training periods opportunities during her/his PhD. Since 2006, $10$ students have benefited of such position. It should be noted that two of them (Boumediene Benyahia and Miled El Hajji) have defended their PhD in 2010 and 2012. They are presently associate professors in Tunisia and Algeria, respectively, and can be said to occupy now `linchpin' positions with respect to the network functioning and to its scientific production, notably in co-advising new students (not less than 3 students, 2 in Tunisia and 1 in Algeria, should begin their PhD soon).\\

\noindent \emph{Promoting cross-research actions} Of course, previously described activities could not be possible without specific financial supports. Presently, the network in no longer supported only by Inria as at its origin but by a consortium including Inra, IRD and foreigner ministries of research (notably in Tunisia, Morocco and Algeria). In addition to this recurrent funding, TREASURE members are trying to find the funding necessary for the running of other projects. A number of important projects have been obtained within the period covered by the present evaluation. In particular the European IRSES COADVISE project (2009-2012), coordinated by Inria, allowed our network to manage 48 months of student exchanges between partners of Tunisia, Algeria, Italy\footnote{POLIMI, Milano, Italy was a founding partner of TREASURE but has officially left since the last $3+3$ call in 2011. However, it should be noticed that we are co-advising Sonia HASSAM, a PhD student actually in Italy and we still keep close technical contacts with our Italian colleagues.} and France. Another important project is a Aires-sud project (2009-2011), obtained in collaboration with our Algerian colleagues and which allowed them to equip their lab with an Anaerobic Membrane BioReactor which has been received within the fall 2013 and which should be run in the next months. Alongside these major successes, a number of bilateral smaller projects allows one to make the network running. For instance, several PHC (Projet Hubert Curien) with Tunisia (2009-2011, 2013-2014) allow the regular exchange of co-advised students for several months.\\\\
\noindent \textbf{DISCO}
All the activities of DISCO are detailed on its 
\href{https://sites.google.com/site/anrdisco/home}{web-site}. \\
The achievements of the three years  of the contract ANR DISCO is the following :
\begin{itemize}
\item 8 workshops. One workshop last  2  days and is devoted to lecture courses and recent contributions of participants.
\item 13 publications out of which 6 are co-signed with members of
  MODEMIC \cite{Art18,Art20,Art32,Art48,Art78,Art19}.
 \item The last workshop has been transform into an international workshop.
\item Some pedagogical texts and codes where realized and are intended to be gathered into a book.
\end{itemize}
$\,$\\
\noindent \textbf{DYMECOS}
All the activities of the Associated Team are detailed on its 
\href{https://sites.google.com/site/eadymecos/}{web-site}
\begin{itemize}
\item 2 publication and 4 preprints related to Ojcetive 3.
\item We started a PhD with a Chilean student Jos\'e Fernandez which, due to his illness, was unfortunately stopped. 
\item Organization of two Franco-Chilean workshops (Valparaiso and Pucon) on wast-ewater treatment processes.
\item Aside this scientific activity, the team strongly got involved at the time of the creation of
  the CIRIC (A Chilean antenna of INRIA) . F. Campillo, C. Lobry and
  P. Gajardo conceived and proposed in 2012 a scientific program which
  included, among others, the Objective 4 of MODEMIC (see section
  \ref{objectif 4} and aggregated, on one side, in Chile the CMM and
  teams of Valparaiso, on the other side, in France, several teams
  from INRIA. This scientific program (see Line
  Natural Resources and
  Bioprocesses\footnote{https://dl.dropboxusercontent.com/u/89779677/Bionature.pdf})
  was not accepted by the CIRIC.
No explanation was given to us.
Our understanding is that our programm had a too fundamental character, INRIA seeming rather to want to develop in Chile exclusively industrial applications
.
\end{itemize}


\subsubsection{Self assessment}
\noindent \textbf{TREASURE}
One of our deception over the last years is our poor success with respect to important project allowing the financial support for the installation of pilot plants in Africa. We have submitted three very important projects of several millions Euros in total in 2010, 2011 and 2012 to ENPI-CBC-MED, Europe FP7 and ANR, respectively, without success although they were all (sometimes very-) positively evaluated. In order to success in the future, a special focus of the actual project concerns the integration of technical skills together with socio-economical and agronomic studies for the integrated solutions developed within the network to be evaluated and tested in practice in the partner's countries. As possible as it may be, we will also try to include industrial partners to valorize the proposed technologies with the help on site in partners from South. Another difficult points to deal with actually are related to the specific situations of several partners: Egypt, Tunisia, Greece but also Algeria since the French intervention in Mali\footnote{since spring 2013, Inra prohibits its researchers to travel in Algeria} experience serious political and/or economical problems. Nevertheless, we plan to submit an important project within the framework of the next French ANR program.\\\\
\noindent \textbf{DISCO}
We consider that this collaboration allowed us to establish a base for solid interdisciplinary research which resulted in several publications. As a matter of fact DISCO strongly contributed to define the orientation of the Objective 4. (see section \ref{objectif 4}). The contract ANR being ended we cannot continue to hold workshops on the same rhythm but the small financing of the network RNSC and the proper resources of the teams will allow to pursue a common reflection (animated by F. Campillo) to the which we shall associate M. Desroches (EPI SYSIPHE).\\\\
\noindent \textbf{DYMECOS} 
The collaboration in  optimal control, recently strengthened by the delegation of T. Bayen, and the recruitment of a post-doc by the CIRIC ( Matthieu Sebbah) is fruitful  but concerns only a small part of the scientific objectives of MODEMIC (namely optimal control) and the possibilities of development of a wider theme seem problematic.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Knowledge dissemination}
\label{section-dissemination}

\subsection{Publications}


\begin{center}
\begin{tabular}{|l|r|r|r|r|} \hline
                                & 2010  & 2011  & 2012  & 2013	\\ \hline \hline
PhD Thesis                      &   1,5   &   1   &  1    &   1  	\\ \hline
H.D.R (*)                       &       &       &       &    	\\ \hline
Journal                         &  13   &   13  &  10    &   12  	\\ \hline
Journal  (!!)                       &  8   &   7  &  6    &   9  	\\ \hline
Conference proceedings (**)     &  8   &   7  &  7    &   8 	\\ \hline
Book chapter                    &       &    2  &       &   1	\\ \hline
Book (written)                  &       &       &       &    	\\ \hline
Book (edited)                   &       &       &       &     	\\ \hline
Patent			        &	&1	&   1	&   1  	\\ \hline
General audience papers         &	&	&	&   2 	\\ \hline
Technical report                &   4   &    5  &   4   &   5 	\\ \hline
Deliverable                     &   1   &    2  &   1   &   1  	\\ \hline

\end{tabular}

(*) HDR Habilitation \`{a} diriger des Recherches\\
(**) Conference with a program committee\\
(!!) In this line we count only our publications which are strictly related to the objectives of the project.

\end{center}

Indicate the major journals in the field and, for each, indicate the
number of papers coauthored by members of the project-team that have
been accepted during the evaluation period.

\begin{enumerate}
\item Ecological Modelling (5)
\item Mathematical biosciences and engineering (4)
\item Bioprocess and Biosystems Engineering (2)
\end{enumerate}

Indicate the major conferences in the field and, for each, indicate
the number of papers coauthored by members of the project-team that
have been accepted during the evaluation period.
\begin{enumerate}
\item CARI: African Conference on Research in Computer Science and
  Applied Mathematics (6). {\em Our strong presence in CARI is related to TREASURE ; it is important for
  us to be present here. CARI is a fully professional conference
  (financially supported by INRIA) which gathers mostly scientists from the African continent.}
 \item NOLCOS: IFAC Symposium on Nonlinear Control Systems (4)
\item CAB: IFAC International Symposium on Computer Applications in
  Biotechnology (4)
\end{enumerate}

\subsection{Software}
\label{section-software}

\begin{description}

\item[] IBM of clonal plant dynamics. This is an Individual-based model simulator for clonal plant growth
developed in 2011 and 2012 in the context of the ANR SYSCOMM project MODECOL, in Matlab\footnote{\url{http://www-sop.inria.fr/members/Fabien.Campillo/software/ibm-clonal/}}.

\item[] IBM's for bacterial growth in the context of the ANR DISCO project.
We proposed: an ``hybrid'' model for the simulation of biofilm growth in a plug flow bioreactor  \cite{Art32} in Java and an IBM for the degradation of one cellulose bead  by cellulolytic bacteria\footnote{\url{http://www-sop.inria.fr/members/Fabien.Campillo/software/ibm-cellulose/}} in Matlab.

\item []
A web service \href{http://vitelbio.itkweb.fr/}{vitelbio.itkweb.fr}
which has been developed within the ARC VITELBIO, in cooperation with the
company ITK\footnote{\url{http://itkweb.com}} and which is currently used as a teaching tool, for Master and PhD classes.


\end{description}

\subsection{Valorization and technology transfer (Socio-economic impact and transfer)}


\begin{description}
\item The TREASURE network is our main operations related to socio-economic
impact and technology transfer: see \ref{objectif 5}.
\item The collaboration with EPI MOISE has been quite successful leading to
the deposit of a patent about an algorithm for ``intelligent'' pumps
for the efficient treatment of water resources. This method can be
typically applied for Chilean lakes, an application that we plan to
launch within a common project with CIRIC INRIA-Chile.
\end{description}

\subsection{Teaching}

\begin{description}

\item Within the TREASURE network we have an important teaching activity : see \ref{objectif 5}.

\item F. Campillo and M. Joannides gives a 20 hours lecture on
  ``Stochastic modeling of ecosystems'' at the Master 2 in
  Biostatistics of Univ. Montpellier II.

\item Fabien Campillo is co-responsible of a 20 hours doctoral module at Univ.
Montpellier II, entitled ``Programmation orientée objet : modélisation
probabiliste \& calculs
numériques en statistique pour la biologie'' (\footnote{\url{https://sites.google.com/site/oopbiol/}}).

\item C. Casenave, F. Campillo, J. Harmand and A. Rapaport are in
  charge of two modules in the new MSc program ``STIC - Environnement'' at
Univ. Montpellier II:
\begin{itemize}
\item[-] Introduction to mathematical Modeling, master I (50 hours)
\item[-] Advanced mathematical Modeling, master II (75 hours)
\end{itemize}

\item C. Casenave, F. Campillo and A. Rapaport are responsible of a 20
  hours doctoral module at Univ. Montpellier II, entitled ``Modeling
  for biology and ecology -- mathematical and computational methods''.

\item A. Rapaport gives 25 hours lecture on differential equations with applications in the ``Practical Mathematics'' module for 1st year students in MSc in Mathematics at Univ. Montpellier II.


\item A. Rapaport gives 12h lectures on mathematical Modeling for 1st year students of SupAgro Montpellier.

\item A. Rapaport gives a 6h lecture about Modeling and numerical
  simulations at the ``EcoSyst\`emes'' Master at Univ. of
  Montpellier II, using the VITELBIO web service (see Section \ref{section-software}). 

\end{description}

\subsection{General audience actions}

%{\footnotesize\sl 
%Mention other dissemination actions:
%general audience papers or talks, podcasts, interviews, videos, web sites, demo%s, etc. TBR.}

\begin{description}
%\item In 2009, Claude Lobry has been invited to a broadcast radio emission of
%  France Culturre about the resetach inn matematics in African countries.
\item In 2013, the team has participated to the writing of a blog for the
  MPT2013, french edition of Mathematics of the Planet Earth 2013.
\item In 2013, the team has participated to the writ-ting of two
  articles TDC magazine dedicated to teachers in secondary classes.
\end{description}

\subsection{Visibility}

%{\footnotesize\sl 
%You could mention here your involvement in publishing activities,
%participation in the organization of workshops/conferences, 
%involvement and responsibilities in your scientific community.
%TBR.}

\begin{description}
\item The team has co-organized with Chilean colleagues the two first
  French-Chilean Workshop on Bioprocess Modelling in Chile en 2010 and
  2012:
\begin{itemize}
\item[-] in 2011:
  \href{https://sites.google.com/site/eadymecos/evenements/workshop/poster_Bioprocess
    modeling-1.pdf?attredirects=0}{site/eadymecos}
\item[-] in 2012:
\href{http://bioprocesos2012.cmm.uchile.cl/}{bioprocesos2012.cmm.uchile.cl}
\end{itemize}
\item The team has organised an International Workshop on Biofilm
  Modelling organised by the DISCO project at Paris in 2013:
\href{https://sites.google.com/site/anrdisco/meetings/workshop-may-2013}{site/anrdisco}
\item The team has organised an invited session about chemostat
  modelling at the 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), Toulouse, 2013.
\item The ``Centre  Interfacultaire Bernoulli'' (CIB) (see
  \href{http://cib.epfl.ch}{cib.epfl.ch}) has for mission to organise
  semester dedicated to mathematics and to their applications. There
  are two semesters a year, endowed with a consequent financing ( 200
  000 FS) and with significant staff (three people). Every three years,
    six projects are selected following a call for tenders. The project
  submitted  by MODEMIC and R. Arditi on ``Mathematics, Computer sciences and Theoretical Ecology'' was accepted in 2013. It will
  be the first semester (July-December 2014) devoted to this theme. It should gather around sixty specialists during a half-dozen workshops. If additional funds are obtained from other sponsors we hope to welcome for the totality of the semester half a dozen post-doc.


\item Team members have participated to several thesis committees:

\begin{description}

\item F. Campillo (referee): M. Xuan-Binh Lam, ``Uncertainty
  quantification for stochastic subspace identification method'',
  Univ. Rennes I, 2011.

\item F. Campillo (referee): Mme Nelly Jean-Baptiste, ``Assimilation
  de donn\'ees pour l'estimation de l'\'etat hydraulique d'un
  am\'enagement hydro\'electrique du Rh\^one \'equip\'e de la commande
  pr\'edictive'', Uni. Toulouse III, 2011.

\item F. Campillo (referee): M. Jean-Louis Marchand, ``Conditionnement
  de processus markoviens'', Univ. de Rennes 1, 2012.

\item F. Campillo (referee): M. Quentin Molto, ``Estimation de
  biomasse en for\^et tropicale humide Propagation des incertitudes dans
  la mod\'elisation de la distribution spatiale de la biomasse en Guyane
  fran\c caise'', Univ. des Antilles et de la Guyane, 2012.


%%%%%%%%%%%%%%%%%%%%%%%

\item J. Harmand (referee): M. Thomas Guélon, ``Déterminer l'influence de la distribution spatiale des bactéries sur les propriétés 
microscopiques de biofilms bactériens par des techniques
d'homogénéisation'', Univ. Blaise Pascal, Univ. Clermont II, 2012.

%\item J. Harmand, T. Sari, C. Lobry (president of the committee): 
%M. Boumediene Benyahia, ``Modélisation et observation
%des bioprocédés à membranes : application à la digestion anaérobie'',
%Univ. Montpellier II and Univ. Tlemcen, Algeria, 2012.

%%%%%%%%%%%%%%%%%%%%%%%

\item C. Lobry (president of the committee): M. Jonathan Rault
  ``Modélisation structurée en taille du zooplancton'' Univ. Nice
  Sophia-Antipolis, 2012.

%%%%%%%%%%%%%%%%%%%%%%%

%\item A. Rapaport (advisor): M. Miled El Hajji, ``Ecologie microbienne
%  des sols : du rôle de la spatialisation des phénomènes sur les
%  interactions microbiennes'', Univ. Montpellier II, 2010.

\item A. Rapaport (examinator): M. Jean-Denis Mathias, ``De la double mod\'elisation \`a
la validation exp\'erimentale par des m\'ethodes de mesure de champs
sans contact du comportement des mat\'eriaux'', th\`ese d'Habilitation
\`a Diriger des Recherches, Univ. B. Pascal, Clermont II, 2011.

\item A. Rapaport (examinator): M. Marc Mazade, ``Ensembles localement
prox-r\'eguliers et in\'equations variationnelles'', Univ. Montpellier
II, 2011.

%\item A. Rapaport (advisor): M.Ihab Haidar, ``Dynamiques microbiennes et
%mod\'elisation des cycles biog\'eochimiques terrestres'',
%Univ. Montpellier II, 2011.

\item A. Rapaport (president of the committee): M. Matthieu Sebbah, ``Stabilité d'inégalités
  variationnelles et prox-régularité, équations de Kolmogorov
  périodiques contrôlées'' , Univ. Montpellier II, 2012.

\item A. Rapaport (referee and president of the committee): Mlle Léontine Nkague Nkamba,
``Robustesse des seuils en épidémiologie et stabilité asymptotique
d'un modèle \`a infectivité et susceptibilité différentielle'',
Univ. Metz and Univ. St-Louis du Sénégal, 2012.

\item A. Rapaport (examinator): M. Benjamin Ivorra, ``Méthodes et techniques de
modélisation, simulation et optimisation appliquées à divers problèmes
industriels'', th\`ese d'Habilitation \`a Diriger des Recherches,
Univ. Montpellier II, 2013.

\item A. Rapaport (referee): M. Derdei Bichara,
``Etude de modèles épidémiologiques: stabilité, observation et estimation de paramètres'',
Univ. Metz, 2013.

%%%%%%%%%%%%%%%%%%%%%%%

%\item T. Sari (examinator): Lyres Nechak, ``Approches robustes du
%  comportement dynamique des systèmes non linéaires : Application aux
%  systèmes frottants'', Univ. Haute Alsace, 2011.

%\item T. Sari (examinator): Jury d'habilitation: Imme van den Berg, ``Discrete %Nonstandard
%Analysis'', Habilitation committee, Univ. of Evora, Portugal, 2012.

%\item T. Sari (referee): Mickael teixeira Alves, ``Des interactions
%  indirectes entre les proies: modélisation et influence du
%  comportement du prédateur commmun, Univ. Nice Sophia Antipolis,
%  2013.


%\item T. Sari (referee): Sihem Kouloughli, ``Optimisation de systèmes
%  automatisés de stockage/déstockage multi allées et à racks
%  glissants'', Univ. of Tlemcen, Algeria, 2013.


\end{description}

\item Team members belong to several evaluation boards:

\begin{description}

\item F. Campillo is member of the NICE (long term invited scientists
  selection); deputy elected member of the INRIA Scientific Council;
  member of the internal communication working group of INRIA Sophia
  Antipolis. F. Campillo was member of the INRA selection board for
  the selection of junior scientists (statistics and modelling).

\item J. Harmand is member of the steering committee of the MEM INRA metaprogram.
\item J. Harmand is member of the scientific committee of the INRA
  Environment and Agronomy department.

\item A. Rapaport is the head of the UMR INRA/SupAgro
  MISTEA since 2009.

\item A. Rapaport is member of the scientific committee of Ecotechnologies dept. of IRSTEA since 2010.

\item A. Rapaport is member of the scientific committee of BIOS
  dept. of CIRAD since 2011.

\item A. Rapaport has been the President of the visiting committee for the
  AERES evaluation of the IRSTEA 'MOTIVE' program in 2012.


\end{description}

%\item Editorial boards}

%\item Invitations prestigieuses

\end{description}


%\subsection{Misc.:}

%\begin{description}
%\item ~
%\end{description}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Funding}
\label{finance}

%{\footnotesize\sl Do not report the yearly budget (``dotation'') allocated by Inria to your team. TBR}

\subsection{Funding external to Inria}
\begin{center}
\begin{tabular}{|l|r|r|r|r|} \hline
(k euros)	                        & 2010 & 2011 & 2012 & 2013	\\ \hline \hline
\multicolumn{5}{| l |}{National initiatives} \\ \hline 
ANR MODECOL	& 62      &  63     &   11    &    	\\ \hline 
ANR DIMIMOS	&  1      &    4    &    6    &    9	\\ \hline
ANR DISCO	&  13     &   12    &   15    &    9	\\ \hline
CNRS PEPI	&         &         &   2     &    1	\\ \hline
INRA AAP        &  15     &   10    &         &   10    \\ \hline
Labex Numev     &         &         &   1     &    2    \\ \hline
RNSC            &   1     &    1    &         &    6    \\ \hline
F. Agropolis    &   3     &         &         &         \\ \hline
\multicolumn{5}{| l |}{European projects}  \\ \hline 
FP7 CAFE	&  17     &   17    &   3     &     1	\\ \hline 
%Tournesol	&         &         &    1    &     	\\ \hline 
\hline
\multicolumn{5}{| l |}{Industrial contracts} \\ \hline \hline
\multicolumn{5}{| l |}{Scholarships} \\ \hline 
INRA        &  40     &  21     &  33     &   33  	\\ 
\hline
Univ. Montpellier        &   33    &  33    &       & 	\\ 
\hline
MESR        &       &  4    &   16    &    16 	\\
\hline
Conycit (Chile)        &   16    &  16     &       &     	\\
\hline
U. Mons  (Belgium)       &      &       &  16     &   16  	\\
\hline
AVERROES	        &      &   9    &   18    & 18 \\
\hline
COADAVISE                &      &  17    &  17     &  22\\
\hline
others (Fr. Amb.)                 &    2  &   2     &         &  10\\
\hline
ANR (postdoc)            &   35 &    42 &    7     &    \\
 \hline \hline
\multicolumn{5}{| l |}{Other external funding} \\ \hline
SticAmSud MOMARE        &  15   &   12  &       &      \\ \hline
3+3 TREASURE 		& 12	& 12	&  12	&    7 	\\ \hline
GuyaSim 		&	&  	& 1	&     	\\ \hline
AVERROES 		&	& 2	& 2	&     	\\ \hline 
\hline
Total			& 265	& 277	& 160	& 160    	\\ \hline 
\end{tabular}
\end{center}

\subsection{Inria competitive funding}


\begin{center}
\begin{tabular}{|l|r|r|r|r|} \hline
(k euros)	                        & 2010 & 2011 & 2012 & 2013	\\ \hline \hline
\multicolumn{5}{| l |}{INRIA Research Initiatives } 	\\ \hline 
ARC $^1$ VITELBIO            	&  23     &       &       &     	\\ \hline 
\hline
\multicolumn{5}{| l |}{Associated teams}   \\ \hline 		
DYMECOS (Chile)		&  20     &   20    &   10    &     	\\ \hline \hline
\multicolumn{5}{| l |}{Scholarships} \\ \hline 
Internship             &       &       &   3    &     	\\ \hline
PhD$^3$ (LIRIMA)              &    1   &    4   &   7    &     	\\ \hline
Post Doc$^4$ (CIRIC)                &       &       &   10    &    42	\\ \hline
\multicolumn{5}{| l |}{Technological development} \\ \hline 
AI $^5$                 		&       &       &       &     	\\ \hline
ADT $^6$				&	&	&	&     	\\ \hline \hline
ODL $^7$			&	&	&	&     	\\ \hline \hline
\multicolumn{5}{| l |}{Other Inria competitive funding} \\ \hline 
LIRIMA NuWat		&	&	& 1	&  16   	\\ \hline
LIRIMA STIC Mada       &       & 10      & 10      &  11             \\ \hline \hline
Total		& 44	& 34	& 41    &  69   	\\ \hline 
\end{tabular}
\end{center}
$^1$ INRIA Cooperative Research Initiative (ARC = Action de Recherche Cooperative). \\
$^2$ Large-scale Initiative Action (AE = Action d'Envergure nationale).\\
%$*$ other than those supported by one of the above projects\\
$^3$ INRIA doctoral research contract (CORDI-S, doctorat Inria sur subvention).\\
$^4$ INRIA postdoctoral research contract (``post-doc Inria sur subvention'').\\
$^5$ Junior engineer supported by INRIA. \\
$^6$ Technological Development Action (ADT = Action de D\'eveloppement Technologique).\\
$^7$ Software Development Operation (ODL = Op\'eration  D\'eveloppement Logiciel). Last ODLs ended in 2010.
\vskip0.5true cm
\noindent
\subsubsection*{National initiatives}
\label{section-national}
\begin{description}


\item ANR MODECOL\footnote{\url{http://ecobio.univ-rennes1.fr/modecol/gb/}} 2009-2012 (program SYSCOMM) [Co-leader 136 kE]\\
The project aims at developing an hybrid model, sufficiently
realistic, that will simulate a prairial ecosystem (modeled through
IBM) correlated through feedback to environmental conditions
(model-ed through PDEs). This approach aims to provide a virtual
laboratory for testing ecological hypothesis on complex ecological
systems. The design of such new ecosystems needs to be optimized for
providing the best ecological services.\\
Research groups: Univ. of Rennes 1 (UMR ECOBIO, project leader), INRIA (EPI MODEMIC,
TOSCA and MAESTRO), Univ. of La Rochelle, Univ. of Houston (Department of Computer Sciences), Univ. of Berkeley (Space sciences laboratory), Univ. of Montréal.
\end{description}

\begin{description}
\item ANR DIMIMOS 2009-2012 (program SYSTERRA) [Partner 20 kE]\\
The main objective is
the grasp the role of the biodiversity in the transformation of the
soil organic matter, in order to better manage the biochemical cycle of the carbon in
agro-ecosystems.\\
Research groups: UMR MSE Microbiologie du Sol et de l'Environnement (Dijon,
project leader), UMR BIOEMCO Biogéochimie et écologie des milieux continentaux
(Thiverval-Grignon), UMR Biogéosciences (Univ. Bourgogne), UREP Unité de Recherche sur
les Ecosystèmes Prairiaux (Inra Theix) and EPI MODEMIC.

\item ANR DISCO\footnote{\url{https://sites.google.com/site/anrdisco/}} 2010-2013 (program SYSCOMM) [Project leader 119 kE ]\\
see section \ref{objectif 5}
Research groups: MODEMIC (project leader), IRSTEA LISC (Clermont) and HBAN
(Antony), CNRS UPTMC ParisVI, INRA LBE (Narbonne), INRA MICALIS
(Massy).

\item CNRS PEPI ASYDE 2013-2014. [Partner 3 kE]\\
Wew tools for the analysis and reduction of the models (flat systems, Lyapunov functions, delayed equations...)
in microbial ecology.

Research groups: L2S (Gif-sur-Yvette, project leader), MIA (INRA Jouy), EPI
MODEMIC and CESAME (Belgique).

\item INRA ENOC AAP\footnote{\url{https://sites.google.com/site/enocprojetreversemodelling/}{site/enocprojetreversemodelling}} 2012-2013 [Project leader 10kE]\\
Funded by the INRA meta-program MEM (metagenomics of microbial
ecosystems), the project is a multidisciplinary approach shared by
microbial ecologists and mathematicians for the reverse modeling of
metagenomic data for microbial resource management. The final
objective is to develop a generic approach for predicting ecosystem
performance from an unknown inoculum.\\
Research groups: MODEMIC (project leader) and LBE (INRA Narbonne).

\item Agropolis Foundation BioInh 2009-2010 [Co-leader, postdoc grant]\\
The project BioInh (Modelling and optimization of bio-conversion of plant materials in inhomogeneous media) proposed by the UMR IATE (Ingénierie des Agropolymères et Technologies Emergentes, Montpellier) and the team MODEMIC has been funded by the Agropolis Foundation (Montpellier) for two years since 2009. The project aims at studying inhomogeneity effects in enzymatic reactors with the help of models of cascade of reactors. The presence of inhibition in the growth function may lead to instabilities and drive the system toward several possible equilibria, one of them only being interesting in terms of yield and productivity. First experiments have been run but have not been finished due the interruption of the hired postdoc for health reasons.\\
Research groups: UMR IATE (project leader), MODEMIC and CNRC-NRC (Canada).

\item Labex Numev. 2012-- [Partner 3 kE\\
Animation of a  a working group on Modelling and numerical
probabilities for ecology and biology\footnote{\url{http://www-sop.inria.fr/members/Fabien.Campillo/gt-modelisation/}}.
Research groups: EPI MODEMIC (project leader), Univ. Montpellier II,
Univ. Montpellier I, CNRS ISEM.

\item RNSC E-MICRAM 2010-11 [Partner  2 kE].\\
The objective of this project supported by the RNSC (National
Network on Complex Systems) is to investigate how complex systems such
as soil microbial ecosystems could be represented by simple models.\\
Research groups: UMR Eco\&Sols (Montpellier, project leader), MODEMIC
and UMR BIOEMCO (Paris Grignon).

\item RNSC MNMs\footnote{\url{http://www-sop.inria.fr/members/Fabien.Campillo/mnms/}} 2013-2014 [Leader 6 kE]\\
This is a partial support of the continuation of DISCO (see section  \ref{objectif 5} )by the RNSC (National
Network on Complex Systems).
Research groups: MODEMIC (project leader), IRSTEA LISC (Clermont),
CNRS LPTMC,
IRSTEA HBAN (Antony), MICALIS (INRA Massy) and LBE (INRA Narbonne).
\end{description}



\subsubsection*{European projects}
\label{section-europe}

\begin{description}
\item CAFE\footnote{\url{http://www.cafe-project.org/}} (Computer-Aided Food processes for control Engineering)
  2009-2013 [Partner 38 kE]\\
This is a Large collaborative project developed in the 7th framework
program of the European Commission (Theme 2: Food, Agriculture and
Fisheries, and Biotechnology), whose objective is to provide new paradigms for the
smart control of food processes, on the basis of four typical
processes in the areas of bio-conversion, separation, preservation and
structuring (resp. wine making, micro-filtration of food beverages,
freeze-drying of lactic acid bacteria and ice cream crystallization. The novelty of the project lies in the capacity of
combining PAT (Process Analytic Technology) and sensing devices with
models and simulation. The team works on the control of multi-stage
bioreactors (for wine making) and the regulation of ice quality (ice
cream crystallization).\\
Partners: Alctra, BIV SA, C-Tech Innovation, IRSTEA, Consejo Superior
de Investigaciones Cientificas (CSIC), Wageningen Univ. and
Research centre, Institut des Sciences et Industries du Vivant et de
l'Environnement Agro Paris Tech, INRA, Povltavske Mlekarny AS, Psutec
SPRL, Societa di Progettazione Elettronica e Software S.C.R.L. SPES,
Telstar Technologies SLU, The Univ. of Manchester, Univ.
Degli Studi di Roma Tor Vergata, Univ. Catholique de Louvain
(project leader) and X-Flow BV.
\end{description}

\subsubsection*{Industrial contracts}

\subsubsection*{ARCs}
\label{section-arc}

\begin{description}
\item ARC VITELBIO\footnote{\url{https://sites.google.com/site/vitelbio}} 2009-2010 [Leader 22 kE]\\
The aim of this action is to study levels of spatial representations in
biochemical models of reactive transport in soil, relevant for
grasping biological and ecological phenomena of microbial activity but
simple enough for simulation and mathematical analyses. In a abstract
way, we have proposed novel representations in terms of network of
chemostats-like and developed a software to explore the effects of the
topology of the network on the performances of the ecosystem.\\
Partners: EPI MODEMIC and IPSO (INRIA Rennes), ITK, UMR Géosciences
(Univ. Rennes 1), UREP (INRA Theix), UMR EcoSols (Montpellier).
\end{description}

\subsubsection*{AEs}
\label{section-ae}

\begin{description}
\item AE Algae in Silico 2013-- [Partner ...]\\
The team is involved in this new large scale action, about Modeling,
simulation and optimisation of micro-algae ecosystems. MODEMIC is
expected to contribute on optimal control, optimal design, simple
spatial coupling of hydrodynamics and model reduction, with the
possibility of co-supervising a PhD student with BIOCORE starting fall
2014.\\
Research groups: BIOCORE (leader), ANGE, DYLISS, MODEMIC, IBIS,
BAMBOO, IFREMER and LOV (Univ. P. \& M. Curie and CNRS, Villefranche-s-mer).
\end{description}

\subsubsection*{Associated teams and other international projects}
\label{section-international}

\begin{description}
\item SticAmsud MOMARE\footnote{\url{http://www-sop.inria.fr/members/Fabien.Campillo/projects/momare/}} 2010-2011 [Leader 27 kE]\\
The project aims at developing a scientific network, consisting of applied mathematicians, around several case studies of estimation and management of renewable resources. It shares different approaches for Modeling renewable resources dynamics and proposing algorithms for identification and control. The mathematical tools are based on dynamical systems theory for deterministic and stochastic systems as well. The project will focus on various ecosystems from microbial ecology to exploited forest, as well as fisheries, etc.\\
Research groups: DIM-CMM, Univ. Chile (Santiago, Chile), UTFSM
(Valparaiso, Chile), PUCV (Santiago, Chile, IMCA (Lima, Peru), IMARPE
(Lima, Peru), PLADEMA (Tandil, Argentina), OPTyCON (Rosario,
Argentina), CESAL (Pinto, Argentina), MODEMIC, CERMICS (Ecole des
Ponts, France), GREQAM (Marseille, France), LAMPS (Univ. Perpignan) and
CERMSEM (CNRS-INRA-Univ. Paris 1).

\item Associated team DYMECOS\footnote{\url{https://sites.google.com/site/eadymecos/}} 2010-2012 (Chile).\\
See section \ref{objectif 5}\\
Research groups: MODEMIC, LBE (INRA Narbonne), DIM (Univ. Chile,
Santiago), UMR CMM (Santagio, Chile), UTFSM (Valparaiso, Chile), PUCV
(Valparaiso, Chile), USACH (Univ. Santiago).

\item LIRIMA STIC-Mada\footnote{\url{http://www.lirima.uninet.cm/index.php/recherche/equipes-de-recherche/stic-mada}} 2010-... (Madagascar).\\
The purpose of the project was to develop land use dynamic model
corresponding to plots located on the edge of the forest corridor linking
the two national parks of Ranomafana and Andringitra in Madagascar. We use
both Markov and semi-Markov models to infer the land-use dynamics. The main
contribution was the co-advising  of a PhD student, Angelo Raherinirina who
defended his thesis in August 2013. This work is done in collaboration with
IRD in Madagascar.\\
%See \href{www.lirima.uninet.cm/index.php/recherche/equipes-de-recherche/stic-mada}{www.lirima.uninet.cm}

\item LIRIMA NuWat\footnote{\url{https://project.inria.fr/nuwat/}} 2013-... (Tlemcen, Algeria).\\
NuWat focuses on the numerical Modeling and simulation of microbial
ecosystems and their application in biotechnology with a focus on solutions
considered as promising for countries of the Maghreb, for instance in
waste-water treatment systems and its reuse in agriculture under
semi-arid climates.
NuWat handles the two following related topics: (1)the elaboration
of numerical hybrid models for simulation of bacterial ecosystems combining
discrete models (for small size populations) and continuous models (for
large size populations, substrate and environment); (2)the systematic
numerical and software development for biotechnology process
control.


\item Euro-Mediterranean 3+3 project TREASURE\footnote{\url{https://project.inria.fr/treasure/}} 2006-2011, renewed in
  2012.\\
The network aims at integrating knowledge on the Modeling, the control and the optimisation of biological systems for the treatment and reuse of waste-waters in countries submitted to semi-arid climates under both socio-economical and agronomic constraints within the actual context of global changes. A special focus concerns the integration of technical skills together with socio-economical and agronomic studies for the integrated solutions developed within the network to be evaluated and tested in practice in the partner's countries and, as possible as it may be within the context of the actual research network, valorizing these proposed technologies with the help of industrial on site in partners from South.\\
Partners: MODEMIC (leader), UMR MISTEA (INRA/SupAgro Montpellier), LBE
(INRA Narbonne), CBS (Sfax, Tunisia), LAMSIN-ENIT (Tunis, Tunisia),
Laboratory of Automatic Control of the Univ. of Tlemcen (Algeria),
Univ. Santiago de Compostella (Spain), CNEREE, (Marrakech,
Morocco), Univ. of Patras (Greece), French Univ. of Egypt
(Cairo, Egypt), NRC (Cairo, Egypt), UCL (Louvain-la-Neuve, Belgium),
POLIMI (Milan, Italy) and Univ. of Provence-IRD (Marseille, France).

\end{description}


\subsubsection*{Other funding}

none

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Objectives for the next four years}

The heart of the activity of MODEMIC is clearly the modeling of
microbial ecosystems and their simulation, that they are natural, by
examples soils, or artificial, essentially the waste-water treatment
and digesters.
Within the activity of modeling we distinguish two main objectives:
\begin{description}
\item[1.] the modeling of ``practical'' questions (for instance are two
  reactors more efficient than one of the same volume? ) and/or the
  modeling of artificial or real ecosystems (such as the ``wine'' process ot soil ecosystems).
\item[2.] the research on modeling tools themselves (such as the numerical hybrid models for simulation of bacterial ecosystems combining discrete and continuous models).
\end{description}

Regarding the first objective, we are going to dedicate an important
effort to the identification for purposes of control of two laboratory
processes to which we have access through our collaborations: the
process of Tlemcen (see TREASURE \ref{objectif 5}) and the ``wine'' process  in Montpellier (see \ref{objectif 3}).
We will continue to address questions on the ``functioning'' of the
ecosystems: which are the qualitative feature in the dynamics which
are changed when we take into account the presence of biofilms or how
to optimize performances of bioprocesses, for instance, how to maximize the production of ``bio-gas''? The control of membrane reactors within the
Euro-Mediterranean network TREASURE let doors open for new challenging modelling
and control problems.

Regarding the second objective, the major outcome of that four years is
that if the traditional continuous models (EDO, EDP) are relevant in
very integrated macroscopic situations they are not suited to fundamental questions in population dynamics.
 If we are not the inventors of this questioning of the pertinence of continuous models  - we can make it start go back at least up to Maurice Bartlett, his students and D. Gillespie and his famous algorithm in the seventies - it seems to be just starting in the field of    the modeling of microbial ecosystems. We think of being part of pioneers, we believe in the future of this direction into which we are very strongly going to put a lot. We will take the opportunity of the creation of NuWat.
 NuWat is a Lirima project for the numerical Modeling and simulation
 of microbial ecosystems and their application in biotechnology that
 will focus on solutions considered as promising for countries of the
 Maghreb. 
%The partners of NuWat are the Automatic Lab of Aboubekr Belkaid University in Tlemcen (Algeria) and MODEMIC. Two topics will be considered: numerical hybrid models for simulation of bacterial ecosystems combining discrete and continuous models ; systematic numerical and software development for biotechnology process control. The NuWat team relies on the TREASURE Mediterranean network.
%Moreover our investment in TREASURE led us to interesting scientific
%questions and allowed us to have students (often excellent) in a
%domain which does not attract the good "European" students trained in
in mathematics and/or computer sciences who prefer subjects more
%"clean" than waste-water treatment processes. 
The NuWat team relies on the TREASURE Mediterranean network, and we are still going to
amplify our investment in this direction. TREASURE owes its existence
to an important effort of INRIA in Africa (LIRIMA and 3+3) seconded
now by INRA; we hope we can continue to take advantage of these
efforts. 

\bigskip


 Our investment in long term dialogue with biologists (and other
 scientists) was paying because he allowed us to approach original
 and important questions  like (more than four years ago) the one of the
 interpretation of  molecular fingerprints, and more recently it is obviously the
 dialogue inside the DISCO project which leads us to revise our methods of
 modeling, and we shall continue in this direction (notably in terms
 of software). In this order of
 idea we have recently organized a ``research school'' of one week
 dedicated to the biologists of the marine research station of Banyuls\footnote{\url{http://lomic.obs-banyuls.fr/fr/test/ecole_chercheur_chemostat.html}}
 with whom we hope to succeed in obtaining an ANR project devoted to
 the modeling of marine microbial ecosystems, a new domain for us.

 The INRIA Cooperative Research Initiative 'Algae in Silico', that has been recently accepted, is also a nice opportunity for the team to
strengthen its relations with the EPI BIOCORE, about the design and
control of photo-bioreactors.

Among our international collaborations, the future of our collaboration with Chile is not entirely in our
hands and relies much on CIRIC's policy regarding fundamental
research. Anyway we shall try to continue our fruitful collaboration
in modelling  and optimal control within the CIRIC project.

 
 A very old collaboration of Inria with ecologists (the COREV network
 presently animated by R. Arditi) initiated (at the beginning of the
 90s) by J-L. Gouz\'e and C. Lobry within the framework of EPI COMORE,
 pursued then by MERE and COMORE raised very recently an important
 success:  the half-year ``Mathematics and computer sciences in
 theoretical ecology'' which we co-organize with R. Arditi (associated
 with D. de
 Angelis and L. Ginzburg) at the Federal Polytechnical School of
 Lausanne (Centre Interfacultaire Bernoulli). The organization of this
 half-year (in July-December 2014) and the preparation of the acts
 will mobilize a great part of our activity for the two years starting just
 now. 



\section{Bibliography of the project-team}

The publications are listed in alphabetical order of the authors in
each category.


\vspace{-5mm}

\begin{category}{Articles in International Journals}
    \SBentries{%
Art159,%
Art8,%
Art9,%
Art16,%
Art18,%
Art20,%
Art165,%
Art32,%
Art39,%
Art42,%
Art43,%
Art45,%
Art48,%
Art50,%
Art51,%
Art70,%
Art71,%
Art72,%
Art160,%
Art74,%
Art76,%
Art77,%
Art78,%
Art85,%
Art86,%
Art88,%
Art91,%
Art101,%
Art105,%
Art107,%
Art109,%
Art115,%
Art123,%
Art125,%
Art132,%
Art133,%
Art134,%
Art164,%
Art135,%
Art136,%
Art141,%
Art142%
}
\end{category}

\begin{category}{Articles in International Journals (in press)}
    \SBentries{%
Art163,%
Art19,%
Art166,%
Art162,%
Art161,%
Art137%
}
\end{category}

\begin{category}{Proceedings in International Conferences}
    \SBentries{%
Proc126,%
Proc127,%
Proc128,%
Proc9,%
Proc10,%
Proc11,%
Proc12,%
Proc131,%
Proc132,%
Proc134,%
Proc23,%
Proc24,%
Proc28,%
Proc29,%
Proc43,%
Misc13,%
Proc49,%
Proc51,%
Proc122,%
Proc52,%
Proc54,%
Proc133,%
Proc53,%
Proc130,%
Proc102,%
Proc106,%
Proc110,%
Proc129,%
Proc112,%
Proc114,%
Proc124%
}
\end{category}

\begin{category}{Proceedings in National Conferences}
    \SBentries{%
Proc8,%
Draft6,%
Proc79%
}
\end{category}


\begin{category}{Book chapters}
    \SBentries{%
Inbook6,%
Inbook2,%
Inbook4%
}
\end{category}

\begin{category}{Research Reports}
    \SBentries{%
Draft12,%
Draft13,%
Draft2,%
Report2,%
Draft15,%
Draft3,%
Report3,%
Draft17,%
Draft18,%
Draft20,%
Draft19,%
Draft4,%
Draft5,%
Draft9,%
Draft10,%
}
\end{category}


%% \begin{category}{Communications without proceedings}
%%     \SBentries{%
%% Proc17,%
%% Proc18,%
%% Proc25,%
%% Proc135,%
%% Proc42,%
%% Proc47,%
%% Proc48,%
%% Proc123,%
%% Proc55,%
%% Proc70,%
%% Proc98,%
%% Proc99,%
%% Proc100,%
%% Proc101,%
%% Proc103,%
%% Proc107,%
%% Proc108,%
%% Proc125,%
%% Proc111%
%% }
%% \end{category}

\begin{category}{Other reports}
    \SBentries{%
Report4,%
Report5,%
%Report9,%
%Report10,%
%Report11,%
%Report12,%
%Report13,%
Report15%
}
\end{category}

\begin{category}{Software}
    \SBentries{%
%Misc6,%
Misc8,%
Misc22%
}
\end{category}

\begin{category}{General Audience Communications}
    \SBentries{%
Art124,%
Inbook5%
}
\end{category}

\begin{category}{Patents}
    \SBentries{%
Misc19,%
Misc27,%
Misc28%
}
\end{category}

\begin{category}{PhD manuscripts}
    \SBentries{%
These20,%
These5,%
These21,%
These6,%
These22,%
These23%
}
\end{category}

\begin{category}{Master reports}
    \SBentries{%
Memoire8,%
Memoire17,%
Memoire19,%
Memoire16,%
Memoire7,%
Memoire9,%
Memoire18%
}
\end{category}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


\nocite{*}


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